Jungjoon Kempthorne LEE
Jungjoon Kempthorne LEEAssistant Professor
[email protected]

Affiliations

Assistant Professor, Department of Biochemistry, Yong Loo Lin School of Medicine, NUS
Principal Investigator, NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)

Biography

Dr. Jungjoon Lee is an assistant professor of Biochemistry and Synthetic Biology for Clinical and Technological Innovation at the National University of Singapore. He trained in chemistry, structural biology, and directed evolution at the University of Cambridge and Stanford University. He previously served as a senior researcher in biotherapeutics at the Samsung Advanced Institute of Technology, where he received the Multiple Citizenship for Outstanding Talent award from the Korean Ministry of Justice, and later led CRISPR platform development at Toolgen, contributing to key patents, publications, and the company’s IPO on KOSDAQ. He is a founding member and former vice chairman of the Korean Association for Genome Editing and currently serves as Vice President Membership of the NUSS Toastmasters Club.

Professional Appointments

  • Senior Director, Research Head Platform Development, Toolgen
  • Senior Researcher, Seoul National University Institute of Molecular Biology and Genetics
  • Senior Researcher, Target Discovery Team, Biotherapeutics Department, Samsung Advanced Institute of Technology

Education

Ph.D. Chemistry (Stanford University)
B.A. & M.Sci. Natural Science Tripos (University of Cambridge)

Research Interest

Our Lab focuses on developing next generation genome editing platforms that combine high activity with maximal precision and safety for therapeutic applications. We engineer CRISPR based editors and related modalities to expand the range of editable targets, improve efficiency in difficult cell types and minimize off target and bystander mutations. A central goal is to create genome editing systems that are both clinically actionable and mechanistically well understood, enabling durable correction of pathogenic alleles in primary cells, organoids and disease relevant models.

To achieve this, the lab integrates directed evolution, high throughput functional screening and quantitative off target profiling such as Extru seq and TAPE seq in human cells and complex tissues. We couple these experimental platforms with computational modeling and AI guided design to discover sequence and structural determinants that govern editing efficiency, specificity and immunogenicity. By iterating between design, large scale perturbation and data driven modeling, the GRIT Lab aims to deliver broadly useful genome editing toolkits and translational pipelines for genetic disease, regenerative medicine and immune engineering.

Current Research Projects

The GRIT Lab’s current research projects are organized into three interconnected themes that span tool invention, optimization, and safety profiling for therapeutic genome editing. 

Genome wide off target detection and safety profiling. 

We develop and refine high throughput experimental platforms such as Extru seq, TAPE seq, and SSID to map genome wide off target effects of diverse CRISPR editors and related nucleases in primary cells, organoids, and other disease relevant systems. By combining these assays with deep sequencing and quantitative modeling, the lab aims to establish robust safety benchmarks and generate training data for predictive algorithms that anticipate off target liabilities prior to clinical translation.  

Invention of new genome editing platforms. 

We mine natural sequence diversity, structural databases, and computational design to discover and engineer novel genome editing systems, including bridge RNA guided transposases and compact CRISPR platforms with improved activity, target range, and compatibility with clinically relevant delivery modalities. These candidates are iteratively evolved and characterized using multiplex functional screens to enable precise gene insertion, scarless repair, and programmable genomic integration in therapeutically relevant cell types.  

Optimization and de immunization of genome editors. 

We use structure aware library design, directed evolution, and high throughput readouts to optimize base editors, prime editors, and nuclease variants for enhanced efficiency, narrowed editing windows, reduced bystander and off target events, and lower predicted immunogenicity. Particular emphasis is placed on engineering inter domain linkers, effector domains, and compact mini binders to achieve therapeutic grade performance in human primary cells and organoid models that capture clinically meaningful constraints. 

Selected Publications

  1. Rebecca Carissa Prajogo, Matthias Lim Boon Han, Jungjoon K. Lee TAPE-seq: A Cell-Based Method for Genome-Wide Off-Target Prediction in Prime Editing, Methods in Molecular Biology (In press)
  2. You-Jeong Kim, Da Young Yoon, Jungjoon K. Lee, Cheulhee Jung*, Aram Chung*, Highly efficient CRISPR-mediated genome editing through microfluidic droplet cell mechanoporation, Nature Communications 15, Article number: 8099, 2024
  3. Hyeji Kwon, Soobon Ko, Kyungsoo Ha, Jungjoon K. Lee*, Yoonjoo Choi*, Assessing the predictive ability of computational epitope prediction methods on Feld1 and other allergens, PlosONE 19(8): e0306254, 2024
  4. Young-hoon Kim, Nahye Kim, Ikenna Okafor, Sungchul Choi, Seonwoo Min, Joonsun Lee, Seung-Min Bae, Keunwoo Choi, Janice Choi, Vinayak Harihar, Youngho Kim, Jin-Soo Kim, Benjamin Kleinstiver, Jungjoon K. Lee*, Taekjip Ha*, Hyongbum Henry Kim*, Sniper2L is a high-fidelity Cas9 variant with high activity, Nature Chemical Biology, 2023
  5. Jeonghun Kwon, Minyoung Kim, Woochang Hwang, Anna Jo, Gue-Ho Hwang, Minhee Jung, Un Gi Kim, Gang Cui, Heonseok Kim, Joon-Ho Eom, Junho K. Hur, Junwon Lee, Youngho Kim, Jin-soo Kim, Sangsu Bae, Jungjoon K. Lee*, Extru-seq: a method for predicting genome-wide Cas9 off-target sites with advantages of both cell-based and in vitro approaches, Genome Biology, 2023, 24, Article number: 4.
  6. Jeonghun Kwon, Minyoung Kim, Seungmin Bae, Anna Jo, Youngho Kim, Jungjoon K. Lee*, TAPE-seq is a cell-based method for predicting genome-wide off-target effects of prime editor, Nature Communications, 2022, 13, Article number: 7975.
  7. Ikenna C Okafor, Digvijay Singh, Yanbo Wang, Minhee Jung, Haobo Wang, John Mallon, Scott Bailey, Jungjoon K. Lee, Taekjip Ha*, Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding, Nucleic Acids Res. 2019 Dec 16; 47(22): 11880–11888.
  8. Joonsun Lee, Minhee Jung, Euihwan Jeong, Jungjoon K. Lee*, Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution. J. Vis. Exp. (144), 2019, e59202,
  9. Jungjoon K. Lee*, Euihwan Jeong, Joonsun Lee, Minhee Jung, Eunji Shin, Young-hoon Kim, Kangin Lee, Inyoung Jung, Daesik Kim, Seokjoong Kim & Jin-Soo Kim*, Directed evolution of CRISPR-Cas9 to increase its specificity, Nature Communications, 2018; 9, Article number: 3048.
  10. Taeyoung Koo1, Jungjoon K. Lee1, Jin-soo Kim*, Measuring and Reducing Off-Target Activities of Programmable Nucleases Including CRISPR-Cas9. Mol Cells. 2015 Jun;38(6):475-81.